title: A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.
abstract: OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA.
authors.forename: Balasundaresan
authors.initials: B
authors.lastname: Dhakshnamoorthy
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA.
authors.forename: Brigitte K
authors.initials: BK
authors.lastname: Ziervogel
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA.
authors.forename: Lydia
authors.initials: L
authors.lastname: Blachowicz
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
mesh_terms: D001965:Bromides / Q000737:chemistry*; D018360:Crystallography, X-Ray; D007477:Ions / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D018272:Porins / Q000737:chemistry*; D011487:Protein Conformation; D012413:Rubidium / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D001965:Bromides; D007477:Ions; C109237:OmpF protein; D018272:Porins; D008274:Magnesium; D012413:Rubidium